Test Pipelines for Genome-Wide SNP Calling from Genotyping-By-Sequencing (GBS) Data for Pinus ponderosa

This study aims to determine the differences of SNP calling pipelines among TASSEL-GBS V2, UNEAK, and Stacks (both reference-based and de novo) for Pinus ponderosa, which has a huge genome and have no available reference genome for this species. We used the reference genome from another closely related species, loblolly pine (Pinus taeda) .